DOI: 10.1186/1471-2105-11-431. Hidden Markov model speed heuristic and iterative HMM search procedure

Hidden Markov model speed heuristic and iterative HMM search procedure

10.1186/1471-2105-11-431

Crossref journal-article

Springer Science and Business Media LLC

BMC Bioinformatics (297)

Bibliography

Johnson, L. S., Eddy, S. R., & Portugaly, E. (2010). Hidden Markov model speed heuristic and iterative HMM search procedure. BMC Bioinformatics, 11(1).

Authors 3

L Steven Johnson (first)
Sean R Eddy (additional)
Elon Portugaly (additional)

References 16 Referenced 1,121

HMMER: biosequence analysis using profile hidden Markov models[ http://hmmer.org/ ]
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 3: 403–410. (10.1016/S0022-2836(05)80360-2) / J Mol Biol by SF Altschul (1990)
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389–3402. 10.1093/nar/25.17.3389 (10.1093/nar/25.17.3389) / Nucleic Acids Res by SF Altschul (1997)
Karplus K, Barrett C, Hughey R: Hidden Markov models for detecting remote protein homologies. Bioinformatics 1998, 14(10):846–856. 10.1093/bioinformatics/14.10.846 (10.1093/bioinformatics/14.10.846) / Bioinformatics by K Karplus (1998)
Scheeff ED, Bourne PE: Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction. BMC Bioinformatics 2006, 7: 410. 10.1186/1471-2105-7-410 (10.1186/1471-2105-7-410) / BMC Bioinformatics by ED Scheeff (2006)
Schaffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, Wolf YI, Koonin EV, Altschul SF: Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res 2001, 29: 2994–3005. 10.1093/nar/29.14.2994 (10.1093/nar/29.14.2994) / Nucleic Acids Res by AA Schaffer (2001)
Holm L, Sander C: Removing near-neighbour redundancy from large protein sequence collections. Bioinformatics 1998, 14(5):423–429. 10.1093/bioinformatics/14.5.423 (10.1093/bioinformatics/14.5.423) / Bioinformatics by L Holm (1998)
Brenner SE, Chothia C, Hubbard TJ: Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc Natl Acad Sci USA 1998, 95(11):6073–6078. 10.1073/pnas.95.11.6073 (10.1073/pnas.95.11.6073) / Proc Natl Acad Sci USA by SE Brenner (1998)
Lo Conte L, Ailey B, Hubbard TJ, Brenner SE, Murzin AG, Chothia C: SCOP: a structural classification of proteins database. Nucleic Acids Res 2000, 28(1):257–259. 10.1093/nar/28.1.257 (10.1093/nar/28.1.257) / Nucleic Acids Res by L Lo Conte (2000)
Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A: The Pfam protein families database. Nucleic Acids Res 2008, 36: D281–8. 10.1093/nar/gkm960 (10.1093/nar/gkm960) / Nucleic Acids Res by RD Finn (2008)
Brenner SE, Koehl P, Levitt M: The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Res 2000, 28: 254–256. 10.1093/nar/28.1.254 (10.1093/nar/28.1.254) / Nucleic Acids Res by SE Brenner (2000)
Chandonia JM, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE: ASTRAL compendium enhancements. Nucleic Acids Res 2002, 30: 260–263. 10.1093/nar/30.1.260 (10.1093/nar/30.1.260) / Nucleic Acids Res by JM Chandonia (2002)
Madera M, Gough J: A comparison of profile hidden Markov model procedures for remote homology detection. Nucleic Acids Res 2002, 30(19):4321–4328. 10.1093/nar/gkf544 (10.1093/nar/gkf544) / Nucleic Acids Res by M Madera (2002)
Pearson WR: Comparison of methods for searching protein sequence databases. Protein Sci 1995, 4: 1145–1160. 10.1002/pro.5560040613 (10.1002/pro.5560040613) / Protein Sci by WR Pearson (1995)
Price GA, Crooks GE, Green RE, Brenner SE: Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap. Bioinformatics 2005, 21: 3824–3831. 10.1093/bioinformatics/bti627 (10.1093/bioinformatics/bti627) / Bioinformatics by GA Price (2005)
Grundy WN: Homology detection via family pairwise search. J Comput Biol 1998, 5(3):479–491. 10.1089/cmb.1998.5.479 (10.1089/cmb.1998.5.479) / J Comput Biol by WN Grundy (1998)

Dates

Type	When
Created	15 years ago (Aug. 19, 2010, 2:13 a.m.)
Deposited	6 years, 7 months ago (Jan. 22, 2019, 8:44 a.m.)
Indexed	9 hours, 2 minutes ago (Aug. 23, 2025, 9:12 p.m.)
Issued	15 years ago (Aug. 18, 2010)
Published	15 years ago (Aug. 18, 2010)
Published Online	15 years ago (Aug. 18, 2010)
Published Print	14 years, 8 months ago (Dec. 1, 2010)

Funders 0

None

BibTeX

@article{Johnson_2010, title={Hidden Markov model speed heuristic and iterative HMM search procedure}, volume={11}, ISSN={1471-2105}, url={http://dx.doi.org/10.1186/1471-2105-11-431}, DOI={10.1186/1471-2105-11-431}, number={1}, journal={BMC Bioinformatics}, publisher={Springer Science and Business Media LLC}, author={Johnson, L Steven and Eddy, Sean R and Portugaly, Elon}, year={2010}, month=aug }

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